Purpose
by Incarnation of Zero
Summary: N and Mewtwo both search for their purpose as fate draws them together, in their mutual quest to stop Cipher and free the shadow Pokemon.
1. Prologue

**Purpose**

_Prologue_

Mewtwo often liked to travel slowly. He knew how fast he could go, and he saw no reason to push himself while wondering aimlessly. Besides, he liked to take in the scenery and the marvels that the world held.

He sometimes felt as if his constant feeling of being out of place meant that he saw the world in a different light to others. Or perhaps that proved he was an independent living being? Not just a mere clone?

Maybe, for once, he should learn to appreciate something without questioning its or his own existence.

The sight he was currently taking in was a man made one; Saffron city, viewed from a distance at night, was quite the spectacular sight.

Mewtwo found himself transfixed by the shining lights and the bustling late night activities. For the people there, this was part of their daily life; it was natural to them. Even at night, people had places to be, work to do, people to meet…

But did he have that sort of familiarity with anything?

A place to call home?

People who needed him?

Sometimes, he'd remember the cloned Pokémon he created- he was responsible for their births, but taking that responsibility and finding a haven for them only put them in harm's way.

They were scattered now- living among other Pokémon, maybe even trainers, finding their own way in this world. And here he was- lost.

Without a purpose.

Only occasionally did he feel the faint connection he had with the clones, but the bond was weakening between them. He could feel them when they were experiencing strong emotions, whether it be happiness, sadness, or…

…danger.

He could feel it now- a sharp, desperate mental cry of help from the surrounding area. Without hesitation, Mewtwo sped towards the source of the plea. Route six wasn't large; he could easily pinpoint the location of the troubled clone in no time-

And then the feeling was gone. Replaced with relief, familiarity, warmth.

Mewtwo was curious now- just what had happened?

The answer came within moments of him landing in a clearing.

A large, marble-white Pokémon stood next to a young man, with long green hair and cap, while a Pikachu dashed off into the surroundings. The white Pokémon had a fierce, ancient presence, but it seemed to…defer to the man?

…Maybe not so much 'defer', but there was certainly a connection between the two.

The man turned to face Mewtwo with a warm smile on his face.

"_Explain what happened here_," Mewtwo demanded telepathically. The man showed no surprise at this, and continued to smile.

"Sometimes, Reshiram can frighten the locals- Pikachu was just slightly distressed, so I calmed him down. If that's what you were referring to…?" the man explained.

"_Why…_"

The man cocked his head in confusion.

"_Why would you show concern for a wild Pokémon?_"

The man spread his arms out in an almost theatrical manner.

"All Pokémon in this world…are my dear, treasured friends."

"_That was a clone that I created._"

"His heart spoke to me much like any other Pokémon."

Mewtwo did not respond, for a moment. The man stepped closer.

"My name is N. What is yours?" he said. Mewtwo wearily regarded him.

"_I am Mewtwo._"

"Mew…two? I've only heard of Mew in the legends."

"_I am a clone of Mew, made as a weapon._"

N looked into Mewtwo's eyes with nothing but kindness.

"You have a voice, and a heart. Why do you call yourself a weapon?"

"_What other Pokémon has the ability to speak?_"

"No, not your mind's voice," N shook his head, "I mean the voice that comes from your heart. Your inner voice."

Mewtwo snorted mentally.

"_Most humans would call you mad._"

"I grew up among Pokémon. I have always been able to speak to my friends. Every one of my friends is wonderful and unique- I love meeting and talking to them."

N's smile had a hint of sadness.

"I once wished to separate people from Pokémon. There are humans who use my friends as weapons and to cause suffering, and it disgusted me to no end. But after a while, I came to realise that there are those who live and share happiness with my friends. Now, I wish for all people to understand the bonds that people can form with Pokémon- and how wonderful they can be!"

N was visibly excited and happy as he spoke. Mewtwo took a moment to process what he'd just heard.

"_The one with you- you called him Reshiram,_" Mewtwo stated, "_Why does he follow you?_"

"Perhaps you should ask him yourself," N replied, smiling up at Reshiram, whose deep blue eyes locked with Mewtwo's. Reshiram had understood the question, Mewtwo could detect.

His answer was…hope.

Reshiram was searching for a hero who could create a new world for people and Pokémon, and N, even when his ideals changed, had a vast amount of potential.

But he needed to learn truth.

"_And that's why you guide him…I see,_" Mewtwo responded, "_And you call him your friend?_"

N nodded.

"_I have met many on my travels...some fear me...some desire to control me...others wished to save me..._"

Mewtwo turned away from N, looking up into the starry night sky.

"_Never have I met one like you, a friend to all Pokémon. Your bond with Reshiram is remarkable- such unwavering belief from an ancient is to be respected, and you are so young..._"

Mewtwo turned his head, looking at N out of the corner of his eye.

"_If you stay on this course, and your feelings for all Pokémon remain this way…I believe we shall meet again._"

And with that, Mewtwo flew off, without once looking back.

N watched him leave, his smile never wavering.

"I, too, believe we shall meet again, my friend…"

* * *

**A/N:** 'What if N met Mewtwo?'  
'What if N met a shadow Pokemon?'

These two questions prompted me to write this story. I've thought of some good ideas, so here's hoping it goes well!

Feedback greatly appreciated!


	2. Fading Green

_1 –Fading Green_

N could feel what Flygon was feeling.

The wind rushing in his face as he soared across the desert.

The sun beating on his back relentlessly.

He could feel it all. He could feel his friend's joy of being so free in the air, as if this was all he needed in life.

Flygon's heart was singing with joy- and N was feeling a very similar feeling.

N had been hearing Pokémon talk about a place of peace and purity, where time seemed to converge. A haven, with a guardian that never show his face.

The Pokémon N had asked about this special place had all been eager to show him, but none more so than this Flygon.

And so, that was where he was headed now; an area in the corner of the desert land of Orre, where no wild Pokémon were said to live.

Eventually, the Flygon exclaimed happily. His eyes were more suited for the desert, and he'd spotted a speck of green in the distance. They were close.

N's own excitement was mirrored by Flygon's, who flew even faster towards their destination. N had no complaints; it was slightly uncomfortable, but it was nothing compared to Flygon's elated feelings.

It only took a few moments before Flygon was circling around a forest.

N looked down on the collection of trees, and noted the small village to the side.

_People co-existing with Pokémon in peace…_

_Perhaps this place truly is paradise…_

Flygon merrily descended into the forest, landing in a small clearing with a shrine in the middle.

N felt oddly drawn to it. A wave of calm flooded through him.

Flygon could feel it too.

The two sat down, as a Skiploom, several Oddish, a Leafeon, a group of Deerling and a few Zigzagoon all gathered around the shrine, seeing the newcomers were no threat.

N could hear the Pokémon's voices. Their hearts were open, their voices cheering in merriment.

He'd seen many things in his journey. He'd seen people and Pokémon interact, he'd seen both happy separately and together.

But nothing had moved him this much for a long time.

The Oddish were climbing onto the other Pokémon's backs, while Skiploom floated around a Deerling, who watched in fascination. Leafeon was laying against Flygon, who seemed to accept this and had wrapped his tail around Leafeon.

A Zigzagoon and a Deerling were chasing each other around the shrine, tirelessly running in circles without end.

The entire scene reminded N of his first memories, when he was brought up in a forest similar to this, among Pokémon. Raised as a child of Pokémon.

Before Ghetsis had found him.

He'd twisted his view of the world, and used him as a tool to 'liberate Pokémon.'

The first time he'd truly been happy, after all those years as King of Team Plasma, was when…

…that trainer…

…had given him a new purpose…

N's eyelids felt heavy; it was starting to get dark, and he'd been traveling all day…

His head was resting against Flygon…

Leafeon had relocated, and was now lying across his lap…

Almost as soon as Flygon had curled his tail around him, he fell asleep.

* * *

The sun had barely made itself known to the morning when the early-rising villagers of Agate could hear the sound of a truck pulling up near the entrance. One or two curious residents watched as two men climbed out of the truck, both disgruntled and bickering with each other.

"How? How did you manage to almost crash us? Twice?" one of the men said.

"You try driving with the best of 'YOU'RE GOING THE WRONG WAY! feat Trudly' blaring in your ear," the other retorted.

"Just let me drive on the way back, Folly," Trudly snapped.

"…What if I say no…?"

"I'll make good use of the CD the boss gave us."

"But you hate his taste in music too- oh, fine. You win. Can we just get this over with?"

Trudly nodded, and the two walked into the village. Any curious villagers had retreated into their homes by now; they could tell trouble when they saw it.

"It's like a friggin' ghost town here…" Folly commented.

"We're meant to find and destroy that shrine thingy, right? Where the hell is that?"

"Beats me. Let's ask for some directions."

"Ask who? Our Pokémon? There's nobody else here."

The two men stood in silence, racking their brains for several minutes, before Folly caught glimpse of a Pachirisu dashing past.

"Follow it!" he yelled, running after it. Trudly looked baffled as he failed to comprehend the scene playing out before him, before realising that Folly was running off without him.

After several minutes of the Pachirisu leading them through the village, they were led down a slope and past a river into a cave, where Folly lost track of the Pokémon. He paused to catch his breath.

"What…was that…?" Trudly gasped, upon catching up.

"I thought…he was gonna lead us to his trainer…" Folly wheezed.

"…Idiot..."

"Sorry…"

When the two had finally stopped breathing so heavily, they glanced around the cave.

"May as well see what's at the other end…" Trudly muttered, leading Folly through the cave.

A warm, comforting feeling flowed through them as they drew closer to the exit.

"No freakin' way…" Trudly breathed in awe.

"I don't believe it…" Folly echoed.

* * *

Moments before this, N was jolted awake by a frantic Pachirisu, who was yelling out a warning. The Pokémon had all gathered around N, Flygon and Leafeon at some point during the night and were all slowly waking up.

Seeming to heed Pachirisu's warnings, most of the Pokémon fled the clearing as N knelt down beside Pachirisu.

"What's happening?" he asked it. Pachirisu frantically pointed at the mouth of the cave leading out of the grove, crying something about dangerous people before darting off.

"No freakin' way…" one voice said, emerging from the cave.

"I don't believe it…" the other one echoed, as two men laid their eyes on the shrine. They hadn't noticed N nor Flygon yet, who were the only others left in the clearing.

"This has gotta be it, Folly."

"Does this make up for my driving earlier?"

"No."

"Trudly…ugh, whatever. Have you got the explosives?"

N darted in front of the shrine, his arms outstretched.

"This is a place of peace and tranquillity, where my friends can find happiness," he said, glaring at Trudly and Folly, "I won't let you harm it!"

"You and your…?" Folly repeated in confusion. Trudly spat in N's direction.

"Listen, kid, this is important business. Something a li'l runt like you wouldn't be able to understand," he said.

"What reason would justify you defiling this paradise?" N snarled.

"Really important reasons."

"You don't know either, Trudly, do you…?" Folly said. He was rewarded with whack on the head.

"Idiot! You're not helping!"

"I don't care anymore. Please leave," N said.

"Oi, I think he's getting' tough with us…"

"Yeah, wow, this is real scary…"

Trudly and Folly simultaneously threw out their Pokémon, a Spinarak and a Whismur respectively.

"Careful now, this could get rough, tough guy," Folly said mockingly.

Flygon made himself known, leaping in front of N and roaring defiantly. Trudly and Folly traded a look, but before they could do anything, N had walked past Flygon.

"It's okay, Flygon. There's no need to fight here."

Flygon looked confused, but did not protest, while N crouched down beside Spinarak and Whismur.

"You can feel it too, right? The calm, purity this place holds?" he said softly, laying his hands on both the Pokémon.

"What is with this nutjob…"

"Ah, whatever. Spinarak, hit him with constrict!"

Spinarak nervously looked between Trudly and N, clearly conflicted. N smiled reassuringly.

"What do you want to do, Spinarak?"

Spinarak and Whismur both turned around, growling at their trainers.

"Wait, what?" Folly said numbly.

"What did you just- ugh, never mind," Trudly sighed, as the two Pokémon were returned to their Pokéballs.

"Dude, maybe you could-"

"Use it? The boss said only when necessary…"

N frowned in confusion as he stood up.

"I'll only ask one more time. Please leave."

"No, not yet…"Trudly grinned, sending out a Makuhita.

But it wasn't a normal Makuhita.

N could see a strange, purple aura emanating from it.

But that wasn't the only strange part.

It had no voice. Its heart was…closed.

"Purple aura? Makuhita…?" he said, feeling uneasy.

"Hit him with shadow rush," Trudly commanded. Makuhita's aura grew darker as he charged at N, crashing into him head-on. Flygon cried out, flying towards the two and swiping Makuhita off N with his tail.

"He attacked me with no regard of his own wellbeing," N muttered, his thoughts spinning, "he…acts like a machine…"

"Keep doing that, Makuhita!" Trudly called out, "now, let's set these explosives."

Makuhita charged at Flygon this time, who dodged and countered with a dragonbreath attack, hitting Makuhita squarely in the face. Makuhita tumbled along the ground, colliding with a tree.

"Flygon, wait…" N said, standing up again, "I want to try and talk to him."

Flygon turned around in protest, pleading N to run. N shook his head, and gently laid his hand on Flygon's back.

"Please…you must save the shrine. Take the explosives they're holding, and take them far away from here."

Flygon whimpered, as Makuhita picked itself up, setting its expressionless gaze on the two.

"It's something only you can do, my friend."

Flygon nodded weakly, and flew towards Trudly and Folly.

"Goodbye, friend, and thank you," N said, a sad smile on his face, "this is a wonderful place you have shown me."

Makuhita threw himself at N, knocking the air out of N's lungs.

"Why, Makuhita? Why is your heart closed? What happened to you?" N wheezed, but was merely struck by Makuhita again.

"Hehe, stupid kid," Folly chuckled, "that Pokémon is awesome. I gotta get me one of them."

"Hold on, the kid said something about purple aura and stuff," Trudly said, holding the bag of explosives.

"He's probably just rambling again."

"But you heard what the boss' boss said, right? If someone can that those Pokémon are different, we have to make sure they don't spread word and stuff."

"Oh yeah, maybe we should-"

Folly was cut off by Flygon, who had swooped in and grabbed the bag of explosives in one smooth motion.

"Hey, what the?"

"Come back here!"

The two yelled and cursed, but Flygon had already left the forest.

"Ah, crud, now what?" Folly moaned hopelessly.

"Let's just grab the kid and run," Trudly groaned.

N had several bruises on his face, and one or two cuts in addition- and was groaning in pain.

But he wasn't giving up.

"What have you done to him?" he said, breathing deeply.

"How the heck would I know? He's just stronger, and more obedient," Trudly responded, "now then…you're coming with us."

Makuhita sent another blow in N's direction, knocking him out cold instantly.

* * *

N awoke to find himself in a small dump of a room.

It was quite the contrast to the forest; in here, furniture and junk was piled up behind him, the floor was cracked in places, and nothing looked like it'd been cleaned for a long time.

N tried to move, but found his arms were tied to the back of the chair he was sat on. The knot was pretty tight, too. He wouldn't be able to get out of it alone.

"Finally awake, are ya?" a huge, muscular man said, standing beside the door.

"Where am I?" N asked, thankful for the fact that at the very least, he wasn't gagged.

"Hehe…you're in paintown now, li'l kid," the man chuckled, cracking his knuckles, "me an' my Pokémon have been needin' a punchin' bag for a while…"

He sent out a Scyther, grinning cruelly. Scyther seemed slightly nervous.

N immediately took interest.

"Scyther…what's wrong?" he said. The man snorted.

"Oh man, they weren't kidding when they called you a psycho."

N ignored this, watching Scyther's reaction.

"I want to save a friend, Scyther," N continued, "these people have done something to him, and maybe others, too."

Scyther nodded, and glanced at the man.

"You don't need to feel obligated to obey him. You should do what you want to do."

"Okay, I've heard enough of this," the man growled, throwing a punch at N's face.

Which Scyther blocked in a flash.

"What the-?"

Scyther snarled, causing the man to yelp in fear, and stumble backwards.

"We should hurry," N urged. Scyther cut the ropes tying N to the chair. Scyther then kicked the man into the heap of trash, saying something about 'a quiet escape'.

The two left the room as silently as possible. Fortunately for them, the corridor was devoid of people.

_Now…where do we go?_

_I want to save that Makuhita quickly, but I don't even know if he's even here._

_Plus, I want Scyther to get out of here quickly…_

"Let's find a way out, Scyther," N whispered, following the corridor to a flight of stairs leading down. The room below was empty, and there were two ways out. One door was open, but a counter blocked the way.

_Easy enough to climb over, I suppose._

"Oh come on, nobody's actually gonna come here!" a voice pleaded from the next room.

"For the last time, no! We have to stay on guard here," another voice argued.

"But- just five minutes?"

"What would the boss say, huh? Would he approve?"

"I- uh…what would he say?"

"…good question…"

Seeing that the two guards were distracting themselves sufficiently, N soundlessly leapt over the counter and beckoned for Scyther to do the same, before both rushed out of the door, outside of the building.

* * *

**A/N:** First chapter!

I loved writing that first part, holy crap. In fact, I loved writing this whole thing.

Anyway, slow/no updates until July, I'm afraid. Exams and stuff.

Feedback much appreciated!


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